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Welcome to the Deltaretrovirus-GLUE User Guide!

Project Overview

Deltaretroviruses are a group of retroviruses that primarily infect mammals, including humans. They are characterized by their ability to establish lifelong infections, often leading to severe diseases such as leukemia and lymphoma. Notable deltaretroviruses include Human T-lymphotropic virus type 1 (HTLV-1), which causes adult T-cell leukemia/lymphoma (ATLL), and Bovine Leukemia Virus (BLV), which induces leukemia in cattle.

Deltaretrovirus-GLUE is a specialized resource designed to support comparative genomic and evolutionary analysis of deltaretroviruses, developed using the GLUE framework.

This resource leverages the GLUE software framework, providing an efficient, standardized platform for analyzing viral genomes. By integrating sequences, annotations, and relational data into a comprehensive, extensible system, Deltaretrovirus-GLUE facilitates advanced computational analysis, reducing the need for manual data handling and enabling researchers to focus on scientific discovery.

Key Features

1. Comprehensive Genomic Database: Deltaretrovirus-GLUE integrates all published sequence data from known deltaretroviruses, providing a robust foundation for comparative genomics research.
2. Standardized Data Formats: All genomic data, including sequences, alignments, and annotations, are standardized, ensuring consistency and interoperability across analyses.
3. Relational Data Structure: The GLUE framework links sequences with complex metadata, allowing for rich, context-driven queries and analyses while minimizing manual pre-processing of datasets.
4. Customizable Comparative Genomics Tools: Researchers can perform customizable genomic analyses, such as evolutionary studies, phylogenetic reconstruction, and genome feature comparisons, tailored to their specific research questions.
5. Extensible Platform: The resource is highly extensible, allowing users to add their own data, annotations, and custom analysis tools, seamlessly integrating them into the core system.
6. Reproducible Workflows Designed to ensure reproducibility, Deltaretrovirus-GLUE enables users to save and share their analyses, allowing for collaboration and transparent research practices.

Getting Started

To begin using Deltaretrovirus-GLUE for comparative genomic analysis, follow these steps:

1. Install GLUE: First, install the GLUE software framework, which forms the backbone of Deltaretrovirus-GLUE. You can either opt for a native installation or use Docker, depending on your preferences and system setup.
2. Download and Import the Core Project: Once GLUE is installed, download the Deltaretrovirus-GLUE core project, which contains the essential deltaretrovirus sequences, annotations, and alignment data. After downloading, import the core project into GLUE to start working with the data.
3. Optionally Build Project Extensions: Deltaretrovirus-GLUE can be extended with additional datasets and analysis tools. For example, you can add the Deltaretrovirus-GLUE-ERV extension, which integrates endogenous retrovirus (ERV) sequences derived from deltaretroviruses.

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